PhysMath Central Blog
Eagle-eyed readers (or those with an RSS feed of latest articles) will have noticed that we have recently published a very interesting paper in PMC Biophysics by Tan and Luo. Handling editor Wei Yang explains below what makes this paper special.
Structural and functional implications of p53 missense cancer mutations
Yuhong Tan, Ray Luo
PMC Biophysics 2009, 2:5 (26 June 2009)
The transcription factor p53 is a central tumor suppressor protein that exerts its functions by relaying upstream stress signals, such as DNA damage, to downstream target genes that control DNA repair, cell cycle arrest, and apoptosis.
Close to 50% of all human cancers have p53 mutations, and 75% of those are missense mutations affecting the p53 DNA-binding core domain of approximately 200 amino acids.
These mutations inactivate the central p53 pathway leading to apoptosis, and allow cancerous cells to proliferate unchecked. Therefore, a long-held goal for anti-cancer therapy is to restore native function to p53 cancer mutants through pharmaceutical interventions, thereby activating apoptosis in cancerous cells and shrinking or killing the tumor.
However, without detailed analysis of the inactivation mechanisms in the cancer mutations, it is difficult to develop therapies targeting p53 cancer mutations.
Tan and Luo conducted a comprehensive computational analysis on all p53 core domain missense mutations to infer their likely inactivation mechanisms. They found that overall, 47.0% non-PRO/GLY mutants are stable and 36.3% mutants are unstable, 12.2% mutants are with 1.0kT < ΔΔG < 3.0kT. Only 4.5% mutants are with no conclusive predictions.
They correlated predicted stability with sequence, structure, and molecular contacts and found that the loss of protein-protein contacts may be an alternative cause for p53 inactivation, in addition to the loss of protein stability and loss of DNA contacts.
Nevertheless, their correlation analysis with clinical data shows that loss of stability and loss of DNA contacts are the two main inactivation mechanisms. Their correlation with functional data also shows that most mutations that retain functions are stable, and most mutations that gain functions are unstable, indicating destabilized and deformed p53 proteins are more likely to find new binding partners.
Posted by Chris Leonard at 14:36 Comments (0)
No charges for PMC Physics A through 2009
We are pleased to announce that PMC Physics A will not be levying any article processing charges for all articles accepted for publication between now and December 31st.
Please pass this news on to your colleagues as this is the perfect opportunity to have your worked published in a fully peer reviewed, open access journal at no cost to you.
View the editorial board here and submit your manuscript here.
Posted by Chris Leonard at 15:29 Comments (0)
PhysMath Central and Open Access
Posted by Chris Leonard at 12:58 Comments (0)
Brian Cox on what went wrong with the LHC
PMC Physics A board member Brian Cox on what went wrong with the LHC last September, how it was fixed and what they are looking forward to now. Originally presented at Ted U in February 2009.
Posted by Chris Leonard at 16:21 Comments (0)
SOAP: Providing a clearer view of the potential of OA
Last month I visited CERN (that's me in front of the CMS experiment) to attend the kick-off meeting of the SOAP project. SOAP (Study of Open Access Publishing) is a 2-year, EU-funded project to study current open access business models and perform a comprehensive survey of attitudes to open access from researchers across all disciplines.
The project will address the need for fact-based evidence of what might and what might not work. The goal of the SOAP project is to document different paths leading to an orderly transition to open access publishing and delineate a number of directions along which publishing may evolve in the future.
This study is being coordinated by CERN, along with the Max Planck Digital Library, Science and Technology Facilities Council and commercial publishers such as Sage, Springer and BioMed Central. Results will be made public in early 2011.
Posted by Chris Leonard at 11:26 Comments (0)
Apologies for the long break between postings, but with moving office, having a baby and being ill, there really don't seem like enough days in the week or hours in the day, but we'll try to make up for it with some good news.
PMC Biophysics, our latest journal covering all aspects of biological physics, has been accepted for coverage in PubMed and PubMed Central. All articles will have their full text available through PubMed Central and PubMed will ensure the abstracts are indexed and available through Medline.
This important step in the journal's development validates the hard work and speedy repsonse of authors and reviewers in getting high-quality work out in very short timeframes. We thank you all.
Posted by Chris Leonard at 10:36 Comments (0)
PhysMath Central, along with our colleagues at BioMed Central and Chemistry Central, are moving to new offices on Friday 20th March. That's the entrance on the right hand side.
Our new contact details will be as follows:
PhysMath Central Ltd
236, Gray's Inn Road
London, WC1X 8HL
UK
+44 20 3192 2000 (switchboard)
+44 20 3192 2013 (customer services)
+44 20 3192 2011 (fax)
Please update your records accordingly. Plus, new Google Streetmap UK view below!
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Posted by Chris Leonard at 09:50 Comments (0)
Recently I have read two very inspiring and stimulating articles which should fire the imagination of any working research scientist.
The first is a transcript of a talk given by Richard Hamming of Bell Labs 23 years ago, entitled "You and Your Research"
This talk centered on Hamming's observations and research on the question ``Why do so few scientists make significant contributions and so many are forgotten in the long run?'' From his more than forty years of experience, thirty of which were at Bell Laboratories, he made a number of direct observations, asked very pointed questions of scientists about what, how, and why they did things, studied the lives of great scientists and great contributions, and has done introspection and studied theories of creativity. The talk is about what he has learned in terms of the properties of the individual scientists, their abilities, traits, working habits, attitudes, and philosophy.
Given its age, it is still amazingly relevant.
The second piece was shorter and more to-the-point, but encapsulated the Hamming talk perfectly: Do Epic Shit.
We hope you'll be inspired!
Posted by Chris Leonard at 17:19 Comments (0)
PMC journals selected for indexing
The first journals launched by PhysMath Central, PMC Physics A and PMC Physics B, have both been selected for inclusion in the updated 2009 versions of the CAS and Scopus databases. Congratulations to the editors, authors and reviewers of both journals for managing this so quickly after launch.
Posted by Chris Leonard at 15:44 Comments (0)
PMC Physics A publishes first review article
PMC Physics A is proud to announce the publication of its first review article. The review, entitled "B meson decays" was written by Elisabetta Barberio of the University of Melbourne and Marina Artuso & Sheldon Stone of Syracuse University, New York.
They discuss the most important physics thus far extracted from studies of B meson decays. Measurements of the four CP violating angles accessible in B decay are reviewed as well as direct CP violation. A detailed discussion of the measurements of the CKM elements Vcb and Vub from semileptonic decays is given, and the differences between resulting values using inclusive decays versus exclusive decays is discussed.
Measurements of rare decays are also reviewed.
They point out where CP violating and rare decays could lead to observations of physics beyond that of the Standard Model in future experiments. If such physics is found by directly observation of new particles, e.g. in LHC experiments, B decays can play a decisive role in interpreting the nature of these particles.
We hope you enjoy the review and look forward to receiving your proposals for future reviews at pmcphysa@physmathcentral.com
Posted by Chris Leonard at 14:40 Comments (0)
New functionality on PhysMath Central
So, in the words of Britney Spears, 'it's been a while' - but here we are with some updates on new outward-facing features we have recently added to PhysMath Central [we're always tinkering with things behind the scenes].
Firstly, the more eagle-eyed among you will have already noticed that the search bar now also sports an 'advanced' option where you can restrict your searches by field or article type or date. We'll be adding more options in to this area soon, so keep your eyes peeled for them.
Secondly, on the right hand side of the homepage you will see a new icon called 'sign up for article alerts'. As you might expect, this allows you to get the titles of the latest articles emailed to you on a schedule of your choosing (every 7, 14 or 30 days, or each time an article is published). This feature, available for each journal PhysMath Central publishes, complements the exisiting RSS feeds for people who prefer to receive updates by email instead.
In the next few weeks, as well as augmenting the functionalities in advanced search, we'll be releasing a whole host of new features including a spanking new design for the whole site, so stay tuned.
Posted by Chris Leonard at 12:01 Comments (0)
Some thoughts on unique author IDs
What I want to write about today is this idea, seemingly fashionable
on blogs and FriendFeed (and PLoS editorials) at the moment, of
authors switching from using their names to identify themselves on
papers to using some other form of ID. The so-called unique author ID
problem.
Now if your name is Xanthe Unique, you might be wondering what the problem is exactly - you just write your name and that's it. It is indexed in Scopus/ISI/whatever subject-specific repository holds sway in your field. However, there is a problem where you may not being credited for your work if any of the following conditions apply:
1 - You share your name with someone else. There is a unusual case in high
energy physics where there are two people called Michel Tytgat working in approximately the same area. Obviously more likely if you
are called John Smith or Jesus Garcia.
2 - Your name is
transliterated. Maybe you are Chinese, Japanese, Korean, Thai, or any
of the places which do not use the Roman character set. In order to be
included in the relevant database/journal/website etc your name needs
to be transliterated to Wei He or whatever. Sometimes it could be
transliterated slightly differently (Wei Hei) and sometimes this
can overlap with shared name problem described above in the western character set where it
never existed in the original language.
3 - You have changed your
name. Most common case here is the women who get married and take their
husband's names. Jayne Smith changes to Jayne Brown, but is still the
same person.
4 - You write your name differently. In order to
identify yourself correctly each time, you need to write your name the
same each time on each paper, or make sure your coauthors do. It could
be the case that the same person is identified as (taking myself as an
example) - C. Leonard, C.J. Leonard, Chris Leonard, Christopher Leonard, Christopher J. Leonard, Christopher James Leonard etc.
So
how to make sure that your work (and citations) are being credited to
you? Well, one idea starting to gain sway is the concept of not
referring to yourself by name, but by some other unique identifier such
as a number.
The advantages are clear. All of the confusions
above could be circumvented and any aliases could be documented on a
unique author homepage.
So how might this happen? Well, this is
something I spent some time thinking about around a year ago at a
discussion about the next generation of bibliographic services in
high-energy physics. I was on a mini team looking at the unique author ID problem and whilst this team was looking at HEP in particular, I was
aware that this was an opportunity to solve the problem for all of
science (note that Scopus has already implemented something like this, all be it not open and behind a subscription wall).
Here, with some image mockups from the time, are some of my thought on the matter.
1 - A central, independent website is in charge of assigning and cataloging all author id numbers.
2 - An author comes to the website to be assigned a unique author id.
3 - The author uses this id in addition to his name on all scientific papers (and publishers publish them alongside the names)
4
- The author has a homepage on this central repository website where he
can list aliases, former institutions, and we can autogenerate a
bibliiogrpahy (which in itself brings up issues about a&i databases
in future). The author can also link to other identifiers about himself
such as OpenID etc. Photos, links to blogs, homepages etc could also be
inserted here. Could also list old email addresses which no longer work.
5 - Anyone can apply for an author id. Authors of grey literature are also encouraged to use this UAID.
6
- This website will not try to validate the applicant as being unique.
It is in their own interests to apply once and use only one UAID number.
Who
would operate this website? A cross-publisher body such as CrossRef
would seem to be one candidate, or otherwise it would be a wholly
independent body - possibly funded by publishers. Clearly I need to
work on it a bit more and I am almost certain it has overlap with many
of the other discussions on the web at the moment, but if I read them
all, I wouldn't be able to get any work done!
I have also decided to share my slides from the time on SlideShare.
Let me know what you think.
Posted by Chris Leonard at 14:45 Comments (9)
From Bill Hooker's blog:
Science Online '09 is less than a week away, and I'm going to be co-moderating an unconference session with Björn Brembs, the theme of which is "Open Access publishing: present and future".
Björn has already put some notes up on the wiki, and there's an interesting contribution from Antony Williams of Chemspider. As both Björn's and Antony's notes make clear, we think the future of Open Access (indeed, all scholarly) publishing will feature prominently the long-overdue death of the Impact Factor. In fact, audience willing, we plan to use some of this session as a sort of preface for Björn's Sunday session with Peter Binfield, which is titled "Reputation, authority and incentives. Or: How to get rid of the Impact Factor".
It's difficult to overstate the extent to which that single figure has come to dominate scholarly and administrative decision making: where to publish, who to fund or promote, which candidate to hire, and so on. It's also difficult to overstate how bad an idea it is to put so much weight on a single journal-level metric derived by undislosed calculations and decisions from a proprietary database.
Read the article in full - and let Bill know your thoughts.
Personally I think OA will simply make it easier to construct new metrics which are much more transparent and therefore inherently superior to proprietary impact factors.
Posted by Chris Leonard at 15:02 Comments (0)
BioMed Central (and PhysMath Central)'s deputy publisher Bryan Vickery was interviewed briefly at Online Information 2008 yesterday. Read the interview with Dirk Kaser here.
Posted by Chris Leonard at 15:25 Comments (0)
In the last few days, people requesting a new password have found that it hasn't been working. This is because we were doing something wrong. Many apologies. It is all fixed now and all passwords should currently work. If you wish, you can still request a new password and that will work too. Thanks for your patience whilst we fixed this.
Posted by Chris Leonard at 17:47 Comments (0)